MolNFT v1 · #70113 · protein

Structure of GTP-bound L129F mutant RAB7

3LAW · RAS-related protein rab-7A: “Structure of GTP-bound L129F mutant RAB7”. X-ray diffraction, 2 ligands (GNP, MG), 12 pockets (best druggability 0.77). MolNFT v1 #70113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LAW
Type: protein
Length: 880 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-7A
UniProt: P51149
Ligands: GNP, MG
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-7A	protein	177	32% helix, 25% strand	P51149
B, E	RAS-related protein rab-7A	protein	175	29% helix, 26% strand	P51149
C	RAS-related protein rab-7A	protein	177	34% helix, 28% strand	P51149
D	RAS-related protein rab-7A	protein	176	32% helix, 26% strand	P51149

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 5 copies · chains A, B, D, C, E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1028	0.77	0.79	100	MG, GNP
2	243	0.73	0.88	38	MG, GNP
3	227	0.73	0.88	36	MG, GNP
4	353	0.70	0.83	46	MG, GNP
5	608	0.70	0.78	59	empty

Interfaces

5 interfaces between chains.

C–E · 718 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 666 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 606 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 576 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 47 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3LAW · Structure of GTP-bound L129F mutant Rab7 · the same entry in another collection · chain E against E, TM-score 1.00
P51149 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P51149) · a predicted model of the same protein · chain C against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P51149
Elsewhere: RCSB PDB 3LAW · PDBe 3LAW · UniProt P51149

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